|
| Status |
Public on Jun 25, 2024 |
| Title |
HaCaT cells, Control, 24h |
| Sample type |
SRA |
| |
|
| Source name |
HaCaT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HaCaT
cell type: Keratinocyte
genotype: WT
treatment: DMSO
|
| Treatment protocol |
After treatment with 60 μg/mL of PAB (Polyopes affinis extract) with TNF-α and IFN-γ (10 ng/mL each) or without, the cells were incubated for 24 h.
|
| Growth protocol |
HaCaT cells were cultured in DMEM supplemented with 10% fetal bovine serum and penicillin-streptomycin (100 U/mL; Gibco). Cells were grown at 37 °C in 100 mm dishes in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and filtered for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19(UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
The read count data were processed based on the quantile-normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor
Gene classification was based on searches performed by DAVID
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Jun 21, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Youn-Jung Kim |
| E-mail(s) |
duckyj@inu.ac.kr
|
| Organization name |
Incheon National University
|
| Street address |
Academyro 119
|
| City |
Incheon |
| ZIP/Postal code |
22012 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE270435 |
Polyopes affinis Suppressed IFN-γ- and TNF-α-Induced Inflammation in Human Keratinocytes via Down-Regulation of the NF-κB and STAT1 Pathways |
|
| Relations |
| SRA |
SRX24998491 |
| BioSample |
SAMN41953806 |
